Locus 5082

Sequence ID 3R_DroMel_CAF1
Location 13,410,253 – 13,410,382
Length 129
Max. P 0.796222
window8282 window8283 window8284

overview

Window 2

Location 13,410,253 – 13,410,346
Length 93
Sequences 6
Columns 100
Reading direction reverse
Mean pairwise identity 80.30
Mean single sequence MFE -31.08
Consensus MFE -19.48
Energy contribution -19.12
Covariance contribution -0.36
Combinations/Pair 1.24
Mean z-score -1.97
Structure conservation index 0.63
SVM decision value 0.60
SVM RNA-class probability 0.796222
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13410253 93 - 27905053
CAACUUUACACGUUAUAGCGACAUAAGUCAGC-CGGC---GGAUGUAGCAACAUAUGUUGCUAACUGCCGACUGGGGUGGCGCAUCCCGA-UCCUGAA--
..........((..((.(((.(((...((((.-((((---((...(((((((....))))))).)))))).)))).))).)))))..)).-.......-- ( -32.50)
>DroVir_CAF1 39884 94 - 1
CAAUUUUACACGUAAUAGCGACAUAAGUCAGUCCGGCAGAGGAUGUCCCGGCAUAUGUCGCUAACUGCCGCUGGGGGUGGCUCAUCCGGGAACG------
...............((((((((((.(((.((((......)))).....))).))))))))))...(((((.....))))).....((....))------ ( -31.10)
>DroGri_CAF1 39906 94 - 1
CAAUUUUACACGUAAUAGCGACAUAAGUCAG-CCAGCAAAGGAUGUCCAGACAUAUGUCGCUAACUGCCACUGG-GGUGGCUCAUUCAGCAGCCAG----
...........((..((((((((((.(((.(-....)...((....)).))).))))))))))...(((((...-.))))).......))......---- ( -28.90)
>DroEre_CAF1 36956 93 - 1
CAACUUUACACGUUAUAGCGACAUAAGUCAGC-CGGC---GGAUGUGGCAACAUAUGUCGCUAACUGCCGAUUGGGGUGGCGCAUCCUGA-UCCUGAC--
..........(((....)))......(((((.-.(((---((..((((((.....))))))...)))))(((..(((((...)))))..)-)))))))-- ( -32.60)
>DroYak_CAF1 41019 95 - 1
CAACUUUACACGUUAUAGUGACAUAAGUCAGC-CGGC---GGAUGUGGCAACAUAUGUCGCUAACUGCCGAUUGGGGUGGCGCAUCCCGA-UCCUGAUCC
........(((......)))......(((((.-.(((---((..((((((.....))))))...)))))((((((((((...))))))))-))))))).. ( -35.20)
>DroAna_CAF1 33784 86 - 1
CAAUUUUACACGUUAUAGCGACAUAAGUCAGC-CUGC---GGAUGUGGCAACAUAUGUCGCUAACUACCGAUUGGGGUAGCUCAUCC--------GUC--
.........(((...((((((((((.((..((-(...---......))).)).)))))))))).(((((......)))))......)--------)).-- ( -26.20)
>consensus
CAACUUUACACGUUAUAGCGACAUAAGUCAGC_CGGC___GGAUGUGGCAACAUAUGUCGCUAACUGCCGAUUGGGGUGGCGCAUCCCGA_UCCUGA___
...............((((((((((.(((.....)))......(((....))))))))))))).(((((......))))).................... (-19.48 = -19.12 +  -0.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 13,410,280 – 13,410,382
Length 102
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 78.83
Mean single sequence MFE -28.95
Consensus MFE -18.10
Energy contribution -18.77
Covariance contribution 0.67
Combinations/Pair 1.13
Mean z-score -1.40
Structure conservation index 0.63
SVM decision value 0.06
SVM RNA-class probability 0.564857
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13410280 102 + 27905053
----CGGCAGUUAGCAACAUAUGUUGCUACAUCC---GCCG-GCUGACUUAUGUCGCUAUAACGUGUAAAGUUGGUAUAAUUCCUGUGGUUGCCAAUGUCUCUGG----GUUCC
----.(((((.(((((((....)))))))...((---((.(-((..((((....(((......)))..))))..).......)).)))))))))...........----..... ( -27.31)
>DroVir_CAF1 39908 98 + 1
----CGGCAGUUAGCGACAUAUGCCGGGACAUCCUCUGCCGGACUGACUUAUGUCGCUAUUACGUGUAAAAUUGUUAUAAUUCUUGCGGUUGCCAUAC-----------GCUC-
----.(((((.((((((((((.(((((.(.......).)))).).....)))))))))).....((((((((((...))))).))))).)))))....-----------....- ( -27.40)
>DroPse_CAF1 36342 110 + 1
UCAGUGCCAGUUAGCGACAUAUGUUGCCACAUCC---GCAG-GCUGACUUAUGUCGCUAUAACGUGUAAAAUUGUUAUAAUUCCUGUGGUUGCCAAUGUCCCUGUUCUCGUUCC
.(((.(.((....(((((....)))))..((.((---((((-(..(((....)))..(((((((........)))))))...))))))).))....)).).))).......... ( -27.00)
>DroGri_CAF1 39931 97 + 1
----UGGCAGUUAGCGACAUAUGUCUGGACAUCCUUUGCUGG-CUGACUUAUGUCGCUAUUACGUGUAAAAUUGUUAUAUGUCUUGCGGUUGCCACAC-----------GUUC-
----((((((.((((((((((.(((.((.((........)).-))))).))))))))))..((((((((.....)))))))).......))))))...-----------....- ( -29.50)
>DroAna_CAF1 33804 102 + 1
----CGGUAGUUAGCGACAUAUGUUGCCACAUCC---GCAG-GCUGACUUAUGUCGCUAUAACGUGUAAAAUUGUUAUAAUUCCUGUGGCUGCCAAUGCCUCGAG----GUCCC
----.((((((((((((((((.((((((......---...)-)).))).))))))))(((((((........))))))).......))))))))...(((....)----))... ( -34.70)
>DroPer_CAF1 37144 110 + 1
UCAGUGCCAGUUAGCGACAUAUGUUGCCACAUCC---GCAG-GCUGACUUAUGUCGCUAUAACGUGUAAAAUUGUUAUAAUUCCUGUGGUUGCCAAUGUCUCUGUUCUCGUUCC
.(((.(.((....(((((....)))))..((.((---((((-(..(((....)))..(((((((........)))))))...))))))).))....)).).))).......... ( -27.80)
>consensus
____CGGCAGUUAGCGACAUAUGUUGCCACAUCC___GCAG_GCUGACUUAUGUCGCUAUAACGUGUAAAAUUGUUAUAAUUCCUGUGGUUGCCAAUGUCUCUG_____GUUCC
.....(((((...((((((((.(((....................))).))))))))(((((((........)))))))..........))))).................... (-18.10 = -18.77 +   0.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 13,410,280 – 13,410,382
Length 102
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 78.83
Mean single sequence MFE -28.92
Consensus MFE -15.11
Energy contribution -15.37
Covariance contribution 0.25
Combinations/Pair 1.15
Mean z-score -1.90
Structure conservation index 0.52
SVM decision value 0.10
SVM RNA-class probability 0.581124
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13410280 102 - 27905053
GGAAC----CCAGAGACAUUGGCAACCACAGGAAUUAUACCAACUUUACACGUUAUAGCGACAUAAGUCAGC-CGGC---GGAUGUAGCAACAUAUGUUGCUAACUGCCG----
.....----...........(((.......((.......)).((((....(((....)))....))))..))-)(((---((...(((((((....))))))).))))).---- ( -26.90)
>DroVir_CAF1 39908 98 - 1
-GAGC-----------GUAUGGCAACCGCAAGAAUUAUAACAAUUUUACACGUAAUAGCGACAUAAGUCAGUCCGGCAGAGGAUGUCCCGGCAUAUGUCGCUAACUGCCG----
-....-----------....((((..(....).......................((((((((((.(((.((((......)))).....))).))))))))))..)))).---- ( -29.40)
>DroPse_CAF1 36342 110 - 1
GGAACGAGAACAGGGACAUUGGCAACCACAGGAAUUAUAACAAUUUUACACGUUAUAGCGACAUAAGUCAGC-CUGC---GGAUGUGGCAACAUAUGUCGCUAACUGGCACUGA
..........(((...(((((((..((.((((..(((((((..........))))))).(((....)))..)-))).---))(((((....)))))...))))).))...))). ( -30.40)
>DroGri_CAF1 39931 97 - 1
-GAAC-----------GUGUGGCAACCGCAAGACAUAUAACAAUUUUACACGUAAUAGCGACAUAAGUCAG-CCAGCAAAGGAUGUCCAGACAUAUGUCGCUAACUGCCA----
-..((-----------(((((....)(....)...............))))))..((((((((((.(((.(-....)...((....)).))).)))))))))).......---- ( -28.60)
>DroAna_CAF1 33804 102 - 1
GGGAC----CUCGAGGCAUUGGCAGCCACAGGAAUUAUAACAAUUUUACACGUUAUAGCGACAUAAGUCAGC-CUGC---GGAUGUGGCAACAUAUGUCGCUAACUACCG----
((..(----((.(.(((.......))).)))).......................((((((((((.((..((-(...---......))).)).))))))))))....)).---- ( -28.80)
>DroPer_CAF1 37144 110 - 1
GGAACGAGAACAGAGACAUUGGCAACCACAGGAAUUAUAACAAUUUUACACGUUAUAGCGACAUAAGUCAGC-CUGC---GGAUGUGGCAACAUAUGUCGCUAACUGGCACUGA
..........(((.(.(((((((..((.((((..(((((((..........))))))).(((....)))..)-))).---))(((((....)))))...))))).)).).))). ( -29.40)
>consensus
GGAAC_____CAGAGACAUUGGCAACCACAGGAAUUAUAACAAUUUUACACGUUAUAGCGACAUAAGUCAGC_CUGC___GGAUGUGGCAACAUAUGUCGCUAACUGCCA____
...................(((((......((((((.....))))))........((((((((((.(((............)))((....)).))))))))))..))))).... (-15.11 = -15.37 +   0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:45:43 2006